ABSTRACT
Mycorrhizal symbioses--the union of roots and soil fungi--are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants. Boreal, temperate and montane forests all depend on ectomycorrhizae. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains approximately 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.
Subject(s)
Basidiomycota/genetics , Basidiomycota/physiology , Genome, Fungal/genetics , Mycorrhizae/genetics , Mycorrhizae/physiology , Plant Roots/microbiology , Symbiosis/physiology , Abies/microbiology , Abies/physiology , Basidiomycota/enzymology , Fungal Proteins/classification , Fungal Proteins/genetics , Fungal Proteins/metabolism , Gene Expression Regulation , Genes, Fungal/genetics , Hyphae/genetics , Hyphae/metabolism , Mycorrhizae/enzymology , Plant Roots/physiology , Symbiosis/geneticsABSTRACT
The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.
Subject(s)
Drosophila melanogaster/genetics , Genome , Sequence Analysis, DNA , Animals , Biological Transport/genetics , Chromatin/genetics , Cloning, Molecular , Computational Biology , Contig Mapping , Cytochrome P-450 Enzyme System/genetics , DNA Repair/genetics , DNA Replication/genetics , Drosophila melanogaster/metabolism , Euchromatin , Gene Library , Genes, Insect , Heterochromatin/genetics , Insect Proteins/chemistry , Insect Proteins/genetics , Insect Proteins/physiology , Nuclear Proteins/genetics , Protein Biosynthesis , Transcription, GeneticABSTRACT
A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.
Subject(s)
Caenorhabditis elegans/genetics , Drosophila melanogaster/genetics , Genome , Proteome , Saccharomyces cerevisiae/genetics , Animals , Apoptosis/genetics , Biological Evolution , Caenorhabditis elegans/chemistry , Caenorhabditis elegans/physiology , Cell Adhesion/genetics , Cell Cycle/genetics , Drosophila melanogaster/chemistry , Drosophila melanogaster/physiology , Fungal Proteins/chemistry , Fungal Proteins/genetics , Genes, Duplicate , Genetic Diseases, Inborn/genetics , Genetics, Medical , Helminth Proteins/chemistry , Helminth Proteins/genetics , Humans , Immunity/genetics , Insect Proteins/chemistry , Insect Proteins/genetics , Multigene Family , Neoplasms/genetics , Protein Structure, Tertiary , Saccharomyces cerevisiae/chemistry , Saccharomyces cerevisiae/physiology , Signal Transduction/geneticsABSTRACT
Collections of nonredundant, full-length complementary DNA (cDNA) clones for each of the model organisms and humans will be important resources for studies of gene structure and function. We describe a general strategy for producing such collections and its implementation, which so far has generated a set of cDNAs corresponding to over 40% of the genes in the fruit fly Drosophila melanogaster.
